The polluted water stunted crops and large numbers of fish being raised in ponds, reports VNS.
General Director of the Sonadezi Long Thanh Company, Do Thi Thu Hang, said it would pay the extra money, totalling $109,000 by the end of this month.
Last June, the company paid 169 households in the Long Thanh District a total of VND11.8 billion (US$561,900) as directed by the Dong Nai Province People's Committee. However, more than 106 other households received no compensation.
The company was set up to treat and discharge waste water created by 42 manufacturing plants in Long Thanh Industrial Park.
However, it was later found that it had dumped the untreated waste water directly into the Ba Cheo Canal for three years up to 2011.
According to the Environmental Police Department, the company dumped 14 million cubic metres of untreated waste over a period of five years.
The 106 householders who missed out in the first settlement voiced their displeasure at a meeting at the commune on Thursday. It was attended by general director Hang, a delegation of Dong Nai members at the National Assembly, and local residents.
Nguyen Van Trai, a resident the Village 2 in Tam An Village, said Environmental Police Department had not clearly informed residents of the company's blame.
Tran Thi Cung, a resident from Village 2, agreed, saying the HCM City-based Institute of Environment and Resources had not assessed the damage properly.
She said householders in the upper area of the polluted canal had been given compensation, but those in the lower area had received nothing.